Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey.

Zhang J, Zhang YP, Rosenberg HF.

Quote

Abstract:

One of the two ribonuclease genes in a leaf-eating monkey has adapted to a role in the digestion of bacterial RNA. Following duplication of the ancestral ribonuclease gene, adaptation occurred through a series of changes in the amino acid sequence of the protein it encodes. This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions.

Quote

A subfamily of Old World monkeys, colobines are unique primates that use leaves rather than fruits and insects as their primary food source; these leaves are then fermented by symbiotic bacteria in the foregut13. Similar to ruminants, colobines recover nutrients by breaking and digesting the bacteria with various enzymes, including pancreatic ribonuclease (RNASE1), which is secreted from the pancreas and transported into the small intestine to degrade RNA.[...]...we detected one RNASE1 gene in each of the 15 non-colobine primates examined, including 5 hominoids, 5 Old World monkeys, 4 New World monkeys and 1 prosimian. We determined the DNA sequences of these RNASE1 genes; the deduced protein sequences are shown in Fig. 1a. The phylogenetic tree of the RNASE1 sequences (Fig. 2a) is consistent with the known species relationships16 at all nodes, with greater than 55% bootstrap support, suggesting that the RNASE1 genes are orthologous. By contrast, two RNASE1 genes were found in the Asian colobine, douc langur (Pygathrix nemaeus). Phylogenetic analysis (Fig. 2a) suggests that these two genes were generated by recent duplication postdating the separation of colobines from other Old World monkeys (cercopithecines). The branch lengths of the gene tree indicate that the nucleotide sequence of one daughter gene (RNASE1) has not changed since duplication, whereas that of the other gene (RNASE1B) has accumulated many substitutions.[...]Taken together, these analyses suggest that the synonymous and noncoding sites at the RNASE1B locus are not subject to selective constraints and that the accelerated evolution of the coding sequence of RNASE1B is due to positive Darwinian selection.[...] Earlier studies showed that, for most mammalian genes, the rate of radical substitution is lower than that of conservative substitution, owing to stronger purifying selection on radical substitution22. In RNASE1B, however, the opposite is found. The number of radical substitutions per site since duplication (0.067) is significantly greater than that (0.012) of conservative substitutions per site (P<0.02; Fisher's exact test). There are nine amino-acid substitutions in the mature peptide of RNASE1B, and seven of them involve charge changes. Unexpectedly, all seven charge-altering substitutions increase the negative charge of the protein.[...]The charge-altering substitutions reduced the net charge of RNASE1B from 8.8 to 0.8 (at pH 7) and the isoelectric point from 9.1 to 7.3 (Fig. 1a). Because RNA is negatively charged, the net charge of RNase influences its interaction with the substrate and its catalytic performance23. We therefore hypothesized that the charge-altering substitutions may have changed the optimal pH of RNASE1B in catalyzing the digestion of RNA.[...]We determined that the optimal pH for human RNASE1 is 7.4, a value that is within the pH range (7.4–8.0) measured in the small intestine of humans24, 25. The same optimal pH was observed for RNASE1 of rhesus monkey and douc langur (Fig. 4a). Probably because of foregut fermentation and related changes in digestive physiology, the pH in the small intestine of colobine monkeys shifts to 6–7 (ref. 13). Notably, the optimal pH for douc langur RNASE1B was found to be 6.3 (Fig. 4a). At pH 6.3, RNASE1B is about six times as active as RNASE1 in digesting RNA, and the difference in their activities is statistically significant (P<0.001, t-test). These results suggest that the rapid amino acid substitutions in RNASE1B were driven by selection for enhanced RNase activity at the relatively low pH environment of the colobine small intestine.

Long story short: Monkey shifts diet from fruits and insects to leaves. This causes foregut fermentation which lowers pH in the digestive tract. A ribonuclease gene duplicates, and one of the duplicates evolves through positive selection for optimal activity at the lower pH.

Another paper concerning this (shorter for those who don't want to plow through the one above) is here: